Uses PLINK clumping method, where variants in LD within a particular window will be pruned. The SNP with the lowest p-value is retained.

ld_clump(
  dat = NULL,
  clump_kb = 10000,
  clump_r2 = 0.001,
  clump_p = 0.99,
  pop = "EUR",
  access_token = NULL,
  bfile = NULL,
  plink_bin = NULL
)

Arguments

dat

Dataframe. Must have a variant name column ("rsid") and pval column called "pval". If id is present then clumping will be done per unique id.

clump_kb

Clumping kb window. Default is very strict, 10000

clump_r2

Clumping r2 threshold. Default is very strict, 0.001

clump_p

Clumping sig level for index variants. Default = 1 (i.e. no threshold)

pop

Super-population to use as reference panel. Default = "EUR". Options are EUR, SAS, EAS, AFR, AMR

access_token

Google OAuth2 access token. Used to authenticate level of access to data

bfile

If this is provided then will use the API. Default = NULL

plink_bin

If null and bfile is not null then will detect packaged plink binary for specific OS. Otherwise specify path to plink binary. Default = NULL

Value

Data frame